When a gene characteristic that is controlled by a single locus has several phenotypes, which are genetically balanced, it is called a polymorphism. Each variable of the polymorphism is called an allele. A polymorphism is attributed not only by phenotype characteristics, or variety of amino acid sequences constructing proteins, but also by DNA base sequences where an amino acid sequence does not have varieties. In most cases, it is detected as cleavage positions of DNA, created by restriction enzymes, that differ from the others.
The HLA molecule of Human MHC molecule (major histocompatibility complex) was found as an antigen against the antibody that reacts in leukoagglutinin during serum treatment, in 1952. The HLA molecule is a gene product controlled by a gene cluster coded by the MHC region, within about 4000 kbp on the 6th chromosome short arm, 6p21.3. The MHC region includes the following 3 regions: 1) Class I gene region controlling HLA-A, B, and C and antigens, which are found on eucaryotic cell membranes, 2) Class II region controlling cell-specific HLA-DP, DQ, and DR antigens, which are found on particular tissues or cells, such as B-cell and macrophage, and 3) Class III gene region controlling complement ingredients and 21-hydroxyilaze.
The Class II molecule is a non-covalent cell membrane antigen made of glycoprotein of 34 kDa (α-chain) and glycoprotein of 29 kDa (β-chain). 7 pieces of α-chain gene and 9 to 12 pieces of β-chain (16 kinds) form clusters to construct a multigene family. On the Class II gene region, each gene lines up as DP-DN-DM-DO-DQ-DR from the centromere side. HLA-DP, DQ, and DR antigens include multiple alloantigens, and mainly the sequences of amino acids of the β-chain (B1) cause a polymorphism. DR and DQ antigens are epitope that reactwith antibodiesproduced from B-cells.
Each HLA molecule includes a form of domain construction with 260 to 370 amino acids. α1(β1), α2(β2) domain, compounded peptide (CP), TM, and CY regions construct the Class II molecule, and α1 and β1 domains configure polymorphism while α2 and β2 domains compose the base of the Class II molecule.
A genetic polymorphism of the HLA molecule is caused by different amino acid sequences coded by the corresponding HLA gene (Gene information regulating the amino acid sequences is written as the base sequence on DNA. A group of three bases, called a “Codon,” is connected as one unit to form a single amino acid.). This is a reflection of an alloantigen with different base sequences, and currently most of the base sequences for alloantigens have been identified. (Tissue Antigen, 45, 258-280, 1995) Regions of polymorphism are found mainly in the α1 and α2 domains of the Class I molecule, and single common variable regions exist on each α1 C-terminal domain and α2 N-terminal domain. In the Class II molecule, the variable regions are found mainly in the α1 domain of the DQα-chain and the β1 domain of DRβ, DQβ, DPβ-chains. (Proc. Natl. Acad. Sci. USA, 84, 6234-6238, 1987). Substitution of the amino acid residue on the variable regions or differences in alloantigens have a direct effect on the affinity of HLA molecules against antigens. Substitution of the amino acid residue on the variable regions or differences in alloantigens also effects an affinity of TCR, which changes the ability of antigen presentations. The fact differentiates immune responses against an exogenous antigen and an autoantigen among individuals with diverse HLA antigens and can induce variety of immune responses.
Brief Description One object of this invention is to elucidate functions controlled by variations of the amino acids on particular positions of particular regions on the HLA genes and the base sequences and to provide usages of the functions in medical field.
This invention has clarified the relationship of particular positions of the amino acids and base sequences and cancer by analysis of clinical phenomenon of cancer patients based on analysis of polymorphisms of the HLA gene.
The following method is provided:    1. A screening method to determine effective cancer curative medicines, comprising:            (1) determining position(s) of polymorphic amino acid(s) in amino acids sequence(s), including at least one of DRB1*gene, DQB1*gene, and DPB1*gene of HLA,        (2) analyzing variations of the polymorphic position(s) of the amino acid(s), and survival results (prognosis, treatment effects) by the cancer treatments [the cancer resection alone (no adjuvant therapy), the anticancer chemotherapy after the cancer resection (Chemotherapy), and the anticancer immunotherapy after the cancer resection (Immunotherapy)],        (3) determining positions of the amino acids and the amino acid(s), which have been estimated to have a statistically significant relationship with the treatments,        (4) creating a three-dimensional structure of amino acid sequences including the amino acids, and        (5) using the interactions of candidate compounds with the three-dimensional structure as a marker.            2. The method according to topic 1, wherein cancer is analyzed by distinguishing stomach cancer and others.    3. The method according to topic 1 or 2, which is carried out by using drug designing techniques based on comparison with the three-dimensional structure of the candidate compounds.    4. The method according to topic 1 to 3, wherein effective cancer curative medicines can suppress and control metastasis of cancer.    5. The method according to topic 1 to 3, wherein effective cancer curative medicines are immunological medicines.    6. The method according to topic 1 to 3, wherein effective cancer curative medicines are chemotherapeutic medicines.    7. The method according to topic 1 to 6, wherein the effectiveness of the cancer curative medicines is measured by:            (1) contacting the candidate compounds and the three-dimensional structure by alignment and variation of each amino acid under a condition in which the interaction is possible,        (2) evaluating the interaction of the three-dimensional structure with the candidate compounds, and detecting a signal of the interaction.            8. The method according to topic 1 to 7, wherein cancer is analyzed by distinguishing stomach cancer and others.    9. The method according to topic 1 to 8, wherein both effectiveness of the anticancer treatments and the variations of the base sequences coding the polymorphic amino acids on any one of DRB1*gene, DQB1*gene, and DPB1*gene of HLA, are analyzed.    10. The method according to topic 1 to 9, wherein both effectiveness of the anticancer treatments and the variations of the base sequences coding the polymorphic amino acids on any one of DRB1*gene, DQB1*gene, and DPB1*gene of HLA, are analyzed.    11. A measuring method for evaluating anticancer treatments, comprising:            (1) determining position(s) of polymorphic amino acid(s) in amino acids sequence(s), including at least one of DRB1*gene, DQB1*gene, and DPB1*gene of HLA,        (2) analyzing variations of the polymorphic position(s) of the amino acid(s), and survival results (prognosis, treatment effects) by the cancer treatments [the cancer resection alone (no adjuvant therapy), the anticancer chemotherapy after the cancer resection (Chemotherapy), the anticancer immunotherapy after the cancer resection (Immunotherapy)],        (3) determining positions of the amino acids and the amino acids, which have been estimated to have a statistically significant relationship with the treatments, and        (4) using the specified positions and the corresponding amino acid(s) as a marker.            12. The method of topic 11, wherein cancer is analyzed by distinguishing stomach cancer and others.    13, A measuring method for evaluating cancer treatments, comprising:            (1) confirming position(s) of polymorphic amino acid(s) in amino acids sequence(s), including at least one of, DRB1*gene, DQB1*gene, and DPB1*gene of HLA,        (2) analyzing variations of the base sequences coding the polymorphic positions of the amino acid, and survival results (prognosis, treatment effects) by the cancer treatments [the cancer resection alone (no adjuvant therapy), the anticancer chemotherapy after the cancer resection (Chemotherapy), the anticancer immunotherapy after the cancer resection (Immunotherapy)],        (3) determining position(s) of the amino acids and the amino acid(s) which have been estimated to have a statistically significant relationship with the treatments, and the corresponding base sequences, and        (4) using the specified positions and the amino acids together with the corresponding base sequences as a marker.            14. The method according to topic 13, wherein cancer is analyzed by distinguishing stomach cancer and others.    15. Clinical measuring reagents comprising a composition:            (1) wherein positions of polymorphic amino acid(s) in amino acids sequence(s), that include at least one of, DRB1*gene, DQB1*gene, and DPB1*gene of HLA have been determined,        (2) wherein the variation of the polymorphic positions of the amino acid, and survival results (prognosis, treatment effects) by the cancer treatments [the cancer resection alone (no adjuvant therapy), the anticancer chemotherapy after the cancer resection (Chemotherapy), the anticancer immunotherapy after the cancer resection (Immunotherapy)] have been analyzed,        (3) wherein the positions of the amino acids and the amino acids, which have been estimated to have a statistically significant relationship with the treatments, have been determined, and        (4) wherein the specified positions and the corresponding amino acids have been used as a marker.            16. The method according to topic 15, wherein cancer is analyzed by distinguishing stomach cancer and others.    17. Clinical measuring reagents comprising a composition:            (1) wherein position(s) of polymorphic amino acid(s) in amino acids sequence(s), that include at least one of DRB1*gene, DQB1*gene, and DPB1*gene of HLA have been confirmed,        (2) wherein the variations of the base sequences coding the polymorphic positions of the amino acid, and survival results (prognosis, treatment effects) by the cancer treatments [the cancer resection alone (no adjuvant therapy), the anticancer chemotherapy after the cancer resection (Chemotherapy), the anticancer immunotherapy after the cancer resection (Immunotherapy)] have been analyzed,        (3) wherein the positions of the amino acids and the base sequences of amino acids which have been estimated to have a statistically significant relationship with the treatments, and the corresponding base sequences have been determined, and        (4) wherein the specified positions and the amino acids together with the base sequences have been used as a marker.            18. The method according to topic 17, wherein cancer is analyzed by distinguishing stomach cancer and others.